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Nickel in PDB 3uyj: Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg

Enzymatic activity of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg

All present enzymatic activity of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg:
1.14.11.27;

Protein crystallography data

The structure of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg, PDB code: 3uyj was solved by X.Su, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.35
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 68.393, 68.393, 266.686, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 25.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg (pdb code 3uyj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg, PDB code: 3uyj:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3uyj

Go back to Nickel Binding Sites List in 3uyj
Nickel binding site 1 out of 2 in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:36.7
occ:1.00
OD2 A:ASP323 1.9 38.7 1.0
O1 A:AKG601 1.9 36.8 1.0
NE2 A:HIS321 2.0 34.1 1.0
O5 A:AKG601 2.1 36.6 1.0
NE2 A:HIS400 2.2 38.3 1.0
O A:HOH5 2.3 39.2 1.0
C1 A:AKG601 2.7 37.4 1.0
C2 A:AKG601 2.7 34.5 1.0
CG A:ASP323 3.0 39.7 1.0
CD2 A:HIS321 3.0 36.0 1.0
CE1 A:HIS321 3.0 38.2 1.0
CD2 A:HIS400 3.2 35.2 1.0
CE1 A:HIS400 3.2 39.8 1.0
OD1 A:ASP323 3.3 44.9 1.0
O A:HOH58 3.8 36.9 1.0
O2 A:AKG601 3.9 35.8 1.0
ND1 A:HIS321 4.1 35.6 1.0
CG A:HIS321 4.1 35.5 1.0
O A:HOH66 4.1 46.2 1.0
C3 A:AKG601 4.2 35.8 1.0
ND1 A:HIS400 4.3 40.8 1.0
CG A:HIS400 4.3 34.8 1.0
CB A:ASP323 4.4 34.3 1.0
CZ2 A:TRP414 4.6 36.9 1.0
H32 A:AKG601 4.6 43.0 1.0
H41 A:AKG601 4.7 39.8 1.0
H31 A:AKG601 4.7 43.0 1.0
H42 A:AKG601 4.8 39.8 1.0
C4 A:AKG601 4.8 33.2 1.0
ND2 A:ASN327 5.0 34.1 1.0
NE1 A:TRP414 5.0 41.2 1.0

Nickel binding site 2 out of 2 in 3uyj

Go back to Nickel Binding Sites List in 3uyj
Nickel binding site 2 out of 2 in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:40.4
occ:1.00
NE2 B:HIS321 2.0 44.8 1.0
OD2 B:ASP323 2.1 42.9 1.0
O5 B:AKG601 2.1 43.4 1.0
O1 B:AKG601 2.1 39.7 1.0
NE2 B:HIS400 2.2 45.5 1.0
O B:HOH19 2.3 37.6 1.0
C2 B:AKG601 2.8 36.9 1.0
C1 B:AKG601 2.8 38.0 1.0
CD2 B:HIS321 3.0 42.4 1.0
CE1 B:HIS321 3.0 44.5 1.0
CG B:ASP323 3.0 41.3 1.0
CE1 B:HIS400 3.2 39.4 1.0
OD1 B:ASP323 3.2 43.6 1.0
CD2 B:HIS400 3.3 45.2 1.0
O2 B:AKG601 4.0 41.1 1.0
ND1 B:HIS321 4.1 44.9 1.0
CG B:HIS321 4.1 43.2 1.0
C3 B:AKG601 4.2 38.3 1.0
O B:HOH124 4.3 49.4 1.0
ND1 B:HIS400 4.3 41.9 1.0
CG B:HIS400 4.4 45.7 1.0
CB B:ASP323 4.4 37.6 1.0
CZ2 B:TRP414 4.6 39.8 1.0
H32 B:AKG601 4.6 46.0 1.0
H41 B:AKG601 4.6 45.7 1.0
H42 B:AKG601 4.8 45.7 1.0
H31 B:AKG601 4.8 46.0 1.0
C4 B:AKG601 4.8 38.1 1.0
NE1 B:TRP414 4.9 41.3 1.0
ND2 B:ASN327 5.0 34.5 1.0

Reference:

X.Su, H.Li. Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg To Be Published.
Page generated: Wed Dec 16 01:28:13 2020

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